Scale bar measurements and pixel sizes of mouse brain images


I am working on a project which requires the use of images from the Allen Brain Atlas and their pixel sizes (micron/pixel).

I have a few queries -

In the URL mentioned above, the scale bar measure for the same image changes when switched between “Annotated” and “Other” (option given at the top-right). Here is an example of image 64 out of 132:

The length of the whole section in case of “Annotated” is roughly half the size of “Other”.

1.) Could you please explain this difference in measurements?

2.) I also wanted to know about the pixel sizes (micron/pixel) of the “downloaded” images using “Other” (not the images in the interactive atlas viewer). Where can I find more about them?

Looking forward to your response!
Many thanks!


From your screenshot I can see you are referring to 2008 version of the Allen Reference Atlas.
This set of images has included as reference to the 2008 published book atlas.
You are correct it appears that the image resolution has not been set correctly.

For your project, I would recommend using a newer a version of the atlases listed in this page
Allen Reference Atlases :: Atlas Viewer (

In particular consider using the Allen Mouse Common Coordinate Framework which is in active use and development.

Allen Mouse CCF - accessing and using related data and tools - Technical - Allen Brain Map Community Forum (

The Allen Mouse Brain Common Coordinate Framework: A 3D Reference Atlas - PubMed (